From: fhh2626_at_gmail.com
Date: Wed Jul 26 2017 - 01:47:09 CDT
What version of NAMD did you use? In NAMD 2.12 or later, you cannot set hidejacobian option when you use eABF. The results always include the contribution of Jacobian term, as what Umbrella Sampling does.
Haohao
fhh2626_at_gmail.com
From: philippe Bourly
Date: 2017-07-25 20:23
To: namd-l; Haohao; coshc Chen
Subject: Re: Re: namd-l: I don't have any eabf output file.
Thank you Haohao.
That was my mistake. I have one more question: When I had the option ‘hidejacobian on’ on my .in file, my number of sample in the count file is close to 0. Do you know why?
Philippe
On Tue, Jul 25, 2017 at 1:20 PM, Haohao <fhh2626_at_gmail.com> wrote:
Hi,
Did you set scriptcolvarforces on in your .in file?
Haohao
On 2017-07-25 18:20 , philippe Bourly Wrote:
Hi,
No, I don't have those files in my output folder.
Philippe
On Tue, Jul 25, 2017 at 12:06 PM, <yjcoshc_at_gmail.com> wrote:
Hi,
Do you have sod2_test.eabf.count and sod2_test.eabf.grad in your output folder?
在 2017年07月22日 02:46, philippe Bourly 写道:
Hello !
I am trying to run an eabf simulation with the RMSD as the collective variable. My calculation is running but I don’t have any output files for the eabf.
In my configuration file I added:
source ./scripts/eabf.tcl
set eabf_inputname 0
set eabf_outputname output/sod2_test.eabf
set eabf_temperature 300
set eabf_outputfreq 10000
But I don’t have any file named sod2_test.eabf in my output folder and I don’t have any errors too. Does anybody know why ?
Below is my colvar configuration file (Does this look correct for you?):
Colvarstrajfrequency 200
Colvarsrestartfrequency 200
colvar {
name rmsd_sod
width 0.1
lowerboundary 1.00
upperboundary 2.00
lowerwallconstant 100.00
upperwallconstant 100.00
extendedLagrangian on
extendedFluctuation 0.1
rmsd {
atoms {
atomsFile ./reference.pdb
atomsCol B
atomsColValue 2.0
}
refpositionsfile ./reference.pdb
}
}
}
abf {
colvars rmsd_sod
FullSamples 5000
historyfreq 10000
}
Thanks,
Philippe
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